Difference between revisions of "Sandbox"

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−
* '''Description:''' glycine betaine-aldehyde dehydrogenase, glycine betaine synthesis <br/><br/>
+
* '''Description:''' glycine decarboxylase (subunit 2) <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''gbsA''
+
|''gcvPB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqhK, gcvP ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glycine betaine-aldehyde dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glycine decarboxylase (subunit 2)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || osmoprotection
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glycine utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 4.713  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 5.283  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1470 bp, 490 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gbsB]]'', ''[[yuaC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqhL]]'', ''[[gcvPA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15084&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14386&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gbsA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gcvPB_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU31060
+
* '''Locus tag:''' BSU24550
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gcvT-gcvPA-gcvPB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11940]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11511]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Betaine aldehyde + NAD<sup>+</sup> + H<sub>2</sub>O = betaine + NADH (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' Glycine + H-protein-lipoyllysine = H-protein-S-aminomethyldihydrolipoyllysine + CO<sub>2</sub> (according to Swiss-Prot)  
  
−
* '''Protein family:''' aldehyde dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:''' C-terminal subunit subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P71016 P71016]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54377 P54377]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31060]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24550]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.8 1.2.1.8]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.4.2 1.4.4.2]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''''' [[gcvT]]-[[gcvPA]]-[[gcvPB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15472076 PubMed]
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] ,  induced by glycine [http://www.ncbi.nlm.nih.gov/sites/entrez/15472076 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' induction requires a co-operatively acting riboswitch [http://www.ncbi.nlm.nih.gov/sites/entrez/15472076 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Erhard Bremer]], University of Marburg, Germany [http://www.uni-marburg.de/fb17/fachgebiete/mikrobio/molmibi homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>9297465, </pubmed>
+
<pubmed>12107147 15472076, </pubmed>
−
# Boch J, Nau-Wagner G, Kneip S, Bremer E. (1997) Glycine betaine aldehyde dehydrogenase from Bacillus subtilis: characterization of an enzyme required for the synthesis of the osmoprotectant glycine betaine. ''Arch Microbiol.'' '''Oct;168(4):''' 282-9. [http://www.ncbi.nlm.nih.gov/sites/entrez/9297465 PubMed]
+
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
 +
# Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. ''Science'' '''306:''' 275-279. [http://www.ncbi.nlm.nih.gov/sites/entrez/15472076 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:18, 8 June 2009

  • Description: glycine decarboxylase (subunit 2)

Gene name gcvPB
Synonyms yqhK, gcvP
Essential no
Product glycine decarboxylase (subunit 2)
Function glycine utilization
MW, pI 54 kDa, 5.283
Gene length, protein length 1464 bp, 488 aa
Immediate neighbours yqhL, gcvPA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GcvPB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU24550

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Glycine + H-protein-lipoyllysine = H-protein-S-aminomethyldihydrolipoyllysine + CO2 (according to Swiss-Prot)
  • Protein family: C-terminal subunit subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: repressed by casamino acids PubMed , induced by glycine PubMed
  • Regulatory mechanism: induction requires a co-operatively acting riboswitch PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Maumita Mandal, Mark Lee, Jeffrey E Barrick, Zasha Weinberg, Gail Mitchell Emilsson, Walter L Ruzzo, Ronald R Breaker
A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
Science: 2004, 306(5694);275-9
[PubMed:15472076] [WorldCat.org] [DOI] (I p)

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

  1. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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